The genus Nectogale, endemic to the Himalayas, Hengduan Mountains, and adjacent ranges, comprises highly specialized semi-aquatic shrews adapted to high-elevation streams. Its diversity has likely been underestimated because of limited sampling and morphological conservatism, leaving species limits and evolutionary relationships unresolved. Here, we combined whole–genome data with morphological evidence to delimit species, infer phylogenetic history, and test for introgression and demographic change. Our results support three species: Nectogale elegans, Nectogale sikhimensis, and a newly identified species, Nectogale jilongensis sp. nov. Divergence-time analyses indicated that the Nectogale lineage diverged from its sister genus in the Middle Miocene (∼14 Ma), followed by diversification between the Late Miocene (∼7 Ma) and Early Pliocene (∼4.5 Ma), broadly coinciding with Himalayan uplift and regional climatic transitions. Admixture analyses and D-statistics (ABBA–BABA tests) indicated significant introgression near species range boundaries, while pairwise sequentially Markovian coalescent (PSMC) analyses revealed contrasting population histories among the three lineages. These results highlight the role of contact zones in facilitating lineage divergence through gene flow, and suggest that regional environmental heterogeneity contributes to distinct evolutionary trajectories across the Himalayas. Our study revises Nectogale taxonomy and clarifies its evolutionary history, offering new insights into diversification in the Himalayan biodiversity hotspot.
Phylogenomic approaches have recently helped to elucidate evolutionary relationships across numerous taxa. Nemouridae (Order Plecoptera) is a Holarctic family divided into two subfamilies, Amphinemurinae and Nemourinae, with seven and 14 extant genera, respectively, plus an additional three genera that are currently known only from the fossil record. The separation of the two subfamilies has been predicated, in part, on the presence of three paraproct lobes on adult males (Amphinemurinae) vs. two (Nemourinae). However, the validity of the two subfamily system in Nemouridae has yet to be holistically addressed using more modern phylogenetic methods, in part, due to limited taxon sampling across the family. In this study, we sequenced the mitochondrial genome of 13 Nemouridae species from China, among which 2 genera (Illiesonemoura, Zapada) were sequenced for the first time. In addition, we sequenced low coverage whole genomes of 10 Nemouridae species from China, including 4 genera (Illiesonemoura, Indonemoura, Sphaeronemoura, Mesonemoura) for the first time. The site-heterogeneous model C20+F+R was applied to a maximum likelihood analysis of Nemouridae for the first time. All conclusions support the monophyly of the Amphinemurinae, but the Nemourinae is not monophyletic. All results confirmed Lednia + (Prostoia + Podmosta) as the sister group to the remaining genera of Nemouridae.
Local adaptation refers to the evolutionary process whereby organisms become better suited to their local environmental conditions, resulting in higher fitness. However, patterns of gene flow among Taxus species and their capacity for local adaptation across current and future climatic landscapes remains unclear. Here, we analyzed dd-RAD sequencing data from 252 individuals from three Taxus species to identify their genetic structure and gene flow patterns, identify climate-associated single-nucleotide polymorphisms (SNPs) across the genome, and predict their spatio-temporal shifts under future climate change. Our study demonstrated that T. qinlingensis harbors the highest genetic diversity and represents a relatively ancient lineage, whereas T. chinensis and T. mairei are closely related. Demographic history analyses indicated that population contractions of the three species were triggered by the Younger Dryas event (12.8–11.5 ka) and the 4.2-kiloyear event. Interspecific gene flow were relatively scarce, with the exception of the LYW and LWT populations, where gene flow was from T. mairei to T. chinensis. Furthermore, 26 common climate-associated SNPs were identified across the three species, primarily associated with metabolic and functional categories, highlighting the role of genetic variation in stress-responsive pathways and climate adaptation. Gradient Forest analysis revealed substantial distributional overlap among the species across the Sichuan Basin and adjacent regions. Notably, the higher predicted genomic offset along the southern, southeastern, and northeastern margins of the Sichuan Basin indicate a greater risk of genetic maladaptation under future climatic changecompared with the northern and western regions. Collectively, these findings reveal the key constraints on the evolutionary potential of three Taxus species and provide an important foundation for their conservation strategies.
The plant cell harbours three genomes, nuclear, plastid and mitochondrial ones, the former being responsible for most plant functions and features. Earlier we sequenced complete plastid and mitochondrial genomes of 91 accessions of pea (Pisum L.), mostly genuine wild and traditional landraces from all over the region of pea traditional cultivation, and reconstructed their phylogenies which turned to be quite discordant. In this work, we undertook a phylogenetic and cluster analysis based on genotyping-by-sequencing (GBS) data on the same set of accessions and compared the result with those based on the plastid and mitochondrial genomes. The GBS phylogenetic tree, overwhelmingly based on the nuclear genome data, well corresponded to the current taxonomy. The plastid and mitochondrial trees showed some discordance, especially the mitochondrial one. The latter suggests cases of exchange of mitochondria between wild and cultivated peas, not accompanied by exchange of plastids or nuclear genes thus posing questions of the underlying mechanisms. The cluster analysis of GBS data is interpreted in terms of clusters evolving from each other and retaining a share of ancestral diversity, rather than through profound hybridisation and admixture. In accordance with the Core Area Hypothesis, the cultivated peas (except for the Abyssinian pea) were monophyletic in the GBS tree and diverged to two main branches immediately after domestication. Attention is drawn to a so far neglected peculiar basally diverged branch of Pisum sativum.
